This issue affects Orion on iOS and iPadOS. I don't know if it affects the desktop version.
I have four bookmarks, all in Favorites: Orion Feedback, Orion User Guide, and two others that link to YouTube videos.
From the menu tab, tap on "Close Tabs & Clear Data" and confirm it. Then, go into Settings -> Privacy, and tap on "Clear History and Website Data". Select all three data types to clear and select "All Time" for the Time Range. When I tap on "Manage websites data", Orion tells me there is no data.
Next, however, tap on "Done" at the top right hand corner to return to the Start Page, enter the multitasking view by swiping up from the bottom of the screen, and close Orion. Open Orion again and return to Settings -> Privacy -> Manage websites data. I always see two entries: kagi.com has "Cache and Cookies" and youtube.com has "Cookies".
You can see the video below.
After clearing website data, and not visiting any websites, I expect to see zero website data. Given my bookmarks, it seems too big a coincidence that kagi and youtube are the two items in website data.
1.3.26 (9) (WebKit 8621.3.11.10.3)
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